ROWLEY — David Johnson ­kayaked across a narrow channel and scrambled up a muddy bank into the heart of New England’s largest salt marsh.

After a 30-minute trek through woods, water, and fiercely biting flies, the Marine Biological Laboratory ­researcher stopped short in front of refrigerator-­sized pieces of marsh bank that had collapsed into two narrow creeks.

It was stark evidence in an unusual scientific experiment that demonstrates the profound damage fertilizers and sewage can wreak on marshes that are critical for protecting young ­marine life and blunting the sea’s fury.

The nine-year study, conducted in the golden-hued Plum Island estuary and published Wednesday in the journal Nature, is the first to show that marshes may be crumbling from the inside out from a massive overload of nutrients.

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“This idea that everyone has to have a bright green lawn is part of what is killing the coast,’’ said lead ­researcher Linda Deegan of the Marine Biological Laboratory Ecosystems Center. “Even if you are 25 miles from the coast, it sinks down into the ground ­water and makes it there.”

The Plum Island estuary, part of New England’s Great Marsh hugging the coastline from Gloucester to Salisbury, is providing scientists a disturbing glimpse into how some of earth’s most productive habitats could fare from a one-two punch. In that scenario, sea-level rise linked to man-made global warming is compounded by other pollution.

The study has particular relevance in the northeastern United States, where recent US Geological Survey research shows sea-level rise is occurring three to four times faster than global rates, probably because of ocean circulation shifts. It ­also comes as communities from Cape Cod to New Hampshire struggle with polluted water­ways from an overload of nutrients generated by sewage and fertilizer.

“The marshes are even more susceptible to climate change because they are deteriorating,’’ Johnson said. “They are not able to keep up with sea-level rise. This is a worldwide issue. . . . We have poured nutrients into [waterways] without under­standing the major ­effects on our coastal eco­systems.”

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Fertilizers and sewage contain nitrogen and phosphorus, nutrients that help lawns and crops grow, but if too much gets into waterways, harmful algae can bloom that suck oxygen out of water and kill marine life.

The experiment, known as TIDE, injected nitrogen and phosphorus, at levels typical of densely developed areas such as Cape Cod, into a 25-acre swath of the marsh on every incoming tide during spring and summer for the last nine years.

For the study, researchers hauled a ton of fertilizer to the salt marsh every four days or so in the spring and summer.(Joanne Rathe/Globe Staff)

It is rare for officials of a relatively pristine ecosystem to give permission for an experiment that could possibly ­destroy parts of that ecosystem, but researchers were able to win the support of the towns of Rowley and Ipswich and the ­Essex County Greenbelt, a nonprofit land conservation trust.

“We know it is broadening the understanding of land use and sea-level rise on the salt marsh,’’ said Ed Becker, executive director of the Greenbelt. “We appreciate it.”

The work was challenging: Every four days or so, the team had to haul about a ton of fertilizer in 50-pound bags to a ­device they named “Frank the Tank” that would release the nutrients into the ecosystem.

A few years after the experiment began, Johnson and ­Deegan noticed wide cracks on the grassy banks of two tidal creeks. Later, those cracks widened and caused parts of the banks to collapse into the muddy creek.

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“We did not anticipate the changes we measured,’’ Deegan said.

Smaller-scale studies had shown that nutrients, much like fertilizer on a lawn, would cause marsh grass to grow more robustly. While that did happen early on, those taller grasses produced fewer roots and rhizomes, a mass of snaking roots that stabilize the banks of creeks. The nitrogen also accelerated the breakdown of leaves and stems in the marsh peat, which also destabilized the creeks’ banks. Soon, they collapsed.

Deegan said marshes would normally rebuild by funneling sediment further inland. But Plum Island, like many marshes, is hemmed in by development, making it impossible to do so.

The study is part of the Plum Island Ecosystem Long-Term Ecological Research program, which conducts basic science in order to better inform coastal managers. It is paid for in part by the National Science Foundation.

The site will still continue to be studied, this time to see how long it will take for the marsh to recover from the intentional flood of nutrients. The answer is important to understanding how weakened tidal marshes could recover if nitrogen stopped pouring into them, Deegan said.

The study may have real policy implications, especially in New England communities struggling with waterways choked by algae sparked in part by nutrients.

For years, governments have often argued that they are respon­sible only for pollution problems in surface waters that can be traced directly to a source, said Christopher Kilian, clean water program director for the Conservation Law Foundation.

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But the study, he said, points to the need for regulatory agencies to deal with nitrogen emanating from a broad array of sources that may have more subtle, yet deeply harmful, ­environmental impacts.

“It creates more urgency to deal with nitrogen and phosphorus pollution pouring into our waterways from so many sources,’’ said Kilian.